It's not really clear which weapons damage the giant sand worms. Longswords don't seem to work, even though they are not a laser weapon. I was able to get through it using one of the Vanduul Blades, but it seemed a little drawn out.
Maybe put a info tablet down in the canyon where the other giant sand worm is that explains what weapons do and do not work against them?
Also, after the battle, it's not very clear that you have to plant a mine in the wall to make it open.